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        <li class="main active"><a href="#clusterprofiler-statistical-analysis-and-visualization-of-functional-profiles-for-genes-and-gene-clusters">clusterProfiler: statistical analysis and visualization of functional profiles for genes and gene clusters</a></li>
        
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            <li><a href="#citation"> Citation</a></li>
        
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<h1 id="clusterprofiler-statistical-analysis-and-visualization-of-functional-profiles-for-genes-and-gene-clusters">clusterProfiler: statistical analysis and visualization of functional profiles for genes and gene clusters</h1>
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<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
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<p><a href="https://bioconductor.org/packages/clusterProfiler"><img alt="" src="https://img.shields.io/badge/release%20version-3.4.4-blue.svg?style=flat" /></a>
<a href="https://github.com/guangchuangyu/clusterProfiler"><img alt="" src="https://img.shields.io/badge/devel%20version-3.5.4-blue.svg?style=flat" /></a>
<a href="https://bioconductor.org/packages/stats/bioc/clusterProfiler"><img alt="" src="https://img.shields.io/badge/download-42676/total-blue.svg?style=flat" /></a>
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<p>The <code>clusterProfiler</code> package implements methods to analyze and
visualize functional profiles of genomic coordinates (supported by
ChIPseeker), gene and gene clusters.</p>
<p><code>clusterProfiler</code> is released within the
<a href="https://bioconductor.org/packages/clusterProfiler">Bioconductor</a>
project and the source code is hosted on
<a href="https://github.com/GuangchuangYu/clusterProfiler"><i class="fa fa-github fa-lg"></i>
GitHub</a>.</p>
<h2 id="author"><i class="fa fa-user"></i> Author</h2>
<p>Guangchuang Yu, School of Public Health, The University of Hong Kong.</p>
<p><a href="https://twitter.com/guangchuangyu"><i class="fa fa-twitter fa-3x"></i></a>
<a href="https://guangchuangyu.github.io/blog_images/biobabble.jpg"><i class="fa fa-wechat fa-3x"></i></a>
<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Guangchuang+Yu[Author+-+Full]"><i class="ai ai-pubmed ai-3x"></i></a>
<a href="https://scholar.google.com.hk/citations?user=DO5oG40AAAAJ&hl=en"><i class="ai ai-google-scholar ai-3x"></i></a>
<a href="https://orcid.org/0000-0002-6485-8781"><i class="ai ai-orcid ai-3x"></i></a>
<a href="https://impactstory.org/u/0000-0002-6485-8781"><i class="ai ai-impactstory ai-3x"></i></a></p>
<h2 id="citation"><i class="fa fa-book"></i> Citation</h2>
<p>Please cite the following article when using <code>clusterProfiler</code>:</p>
<p><a href="http://dx.doi.org/10.1089/omi.2011.0118"><img alt="" src="https://img.shields.io/badge/doi-10.1089/omi.2011.0118-blue.svg?style=flat" /></a>
<a href="https://www.altmetric.com/details/681089"><img alt="" src="https://img.shields.io/badge/Altmetric-23-blue.svg?style=flat" /></a>
<a href="http://online.liebertpub.com/action/showMostCitedArticles?journalCode=omi"><img alt="" src="https://img.shields.io/badge/2nd%20most%20cited%20paper-in%20OMICS-blue.svg?style=flat" /></a>
<a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=2349076811020942117"><img alt="citation" src="https://img.shields.io/badge/cited%20by-215-blue.svg?style=flat" /></a>
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<a href="http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&amp;customersID=RID&amp;IsProductCode=Yes&amp;product=WOS&amp;Init=Yes&amp;Func=Frame&amp;DestFail=http%3A%2F%2Fwww.webofknowledge.com&amp;action=retrieve&amp;SrcApp=RID&amp;SrcAuth=RID&amp;SID=Y2CXu6nry8nDQZcUy1w&amp;UT=WOS%3A000303653300007"><img alt="" src="https://img.shields.io/badge/ESI-Highly%20Cited%20Paper-blue.svg?style=flat" /></a></p>
<p><strong>Yu G</strong>, Wang L, Han Y and He Q<sup>*</sup>. clusterProfiler: an R
package for comparing biological themes among gene clusters. <strong><em>OMICS: A
Journal of Integrative Biology</em></strong>. 2012, 16(5):284-287.</p>
<h2 id="featured-articles"><i class="fa fa-pencil"></i> Featured Articles</h2>
<p><img src="https://guangchuangyu.github.io/featured_img/clusterProfiler/elife-02077-fig5-v1.jpg" width="650"></p>
<p><i class="fa fa-hand-o-right"></i> Find out more on
<i class="fa fa-pencil"></i> <a href="https://guangchuangyu.github.io/clusterProfiler/featuredArticles/">Featured
Articles</a>.</p>
<h2 id="installation"><i class="fa fa-download"></i> Installation</h2>
<p>Install <code>clusterProfiler</code> is easy, follow the guide on the <a href="https://bioconductor.org/packages/clusterProfiler/">Bioconductor
page</a>:</p>
<pre><code class="r">## try http:// if https:// URLs are not supported
source(&quot;https://bioconductor.org/biocLite.R&quot;)
## biocLite(&quot;BiocUpgrade&quot;) ## you may need this
biocLite(&quot;clusterProfiler&quot;)
</code></pre>

<h2 id="overview"><i class="fa fa-cogs"></i> Overview</h2>
<h4 id="supported-analyses"><i class="fa fa-angle-double-right"></i> Supported Analyses</h4>
<ul>
<li>Over-Representation Analysis</li>
<li>Gene Set Enrichment Analysis</li>
<li>Biological theme comparison</li>
</ul>
<h4 id="supported-ontologiespathways"><i class="fa fa-angle-double-right"></i> Supported ontologies/pathways</h4>
<ul>
<li>Disease Ontology (via
    <a href="https://www.bioconductor.org/packages/DOSE">DOSE</a>)</li>
<li><a href="http://ncg.kcl.ac.uk/">Network of Cancer Gene</a> (via
    <a href="https://www.bioconductor.org/packages/DOSE">DOSE</a>)</li>
<li><a href="http://www.disgenet.org/web/DisGeNET/menu/home">DisGeNET</a> (via
    <a href="https://www.bioconductor.org/packages/DOSE">DOSE</a>)</li>
<li>Gene Ontology (supports many species with GO annotation query online
    via
    <a href="https://bioconductor.org/packages/AnnotationHub/">AnnotationHub</a>)</li>
<li>KEGG Pathway and Module with latest online data (supports more than
    4000 species listed in
    <a href="http://www.genome.jp/kegg/catalog/org_list.html">http://www.genome.jp/kegg/catalog/org_list.html</a>)</li>
<li>MeSH enrichment analysis (via
    <a href="https://www.bioconductor.org/packages/meshes">meshes</a>)</li>
<li>Reactome Pathway (via
    <a href="https://www.bioconductor.org/packages/ReactomePA">ReactomePA</a>)</li>
<li>DAVID (via
    <a href="https://www.bioconductor.org/packages/RDAVIDWebService">RDAVIDWebService</a>)</li>
<li><a href="http://software.broadinstitute.org/gsea/msigdb">Molecular Signatures
    Database</a><ul>
<li>hallmark gene sets</li>
<li>positional gene sets</li>
<li>curated gene sets</li>
<li>motif gene sets</li>
<li>computational gene sets</li>
<li>GO gene sets</li>
<li>oncogenic signatures</li>
<li>immunologic signatures</li>
</ul>
</li>
<li>Other Annotations<ul>
<li>from other sources (e.g.
    <a href="http://www.disgenet.org/web/DisGeNET/menu/home">DisGeNET</a> as
    <a href="https://guangchuangyu.github.io/2015/05/use-clusterprofiler-as-an-universal-enrichment-analysis-tool/">an
    example</a>)</li>
<li>user's annotation</li>
<li>customized ontology</li>
<li>and many others</li>
</ul>
</li>
</ul>
<h4 id="visualization"><i class="fa fa-angle-double-right"></i> Visualization</h4>
<ul>
<li>barplot</li>
<li>cnetplot</li>
<li>dotplot</li>
<li>enrichMap</li>
<li>gseaplot</li>
<li>plotGOgraph (via
    <a href="https://www.bioconductor.org/packages/topGO">topGO</a> package)</li>
<li>upsetplot</li>
</ul>
<h4 id="useful-utilities"><i class="fa fa-angle-double-right"></i> Useful utilities:</h4>
<ul>
<li>bitr (Biological Id TranslatoR)</li>
<li>compareCluster (biological theme comparison)</li>
<li>dropGO (screen out GO term of specific level or specific term)</li>
<li>go2ont (convert GO ID to Ontology)</li>
<li>go2term (convert GO ID to descriptive term)</li>
<li>gofilter (restrict result at specific GO level)</li>
<li>gsfilter (restrict result by gene set size)</li>
<li>simplify (remove redundant GO terms, supported via
    <a href="https://www.bioconductor.org/packages/GOSemSim">GOSemSim</a>)</li>
</ul>
<p><i class="fa fa-hand-o-right"></i> Find out details and examples on
<i class="fa fa-book"></i>
<a href="https://guangchuangyu.github.io/clusterProfiler/documentation/">Documentation</a>.</p>
<h2 id="related-tools"><i class="fa fa-wrench"></i> Related Tools</h2>
<ul class="fa-ul">
    <li><i class="fa-li fa fa-angle-double-right"></i><a href="https://guangchuangyu.github.io/DOSE">DOSE</a> for Disease Ontology Semantic and Enrichment analyses</li>
    <li><i class="fa-li fa fa-angle-double-right"></i><a href="https://guangchuangyu.github.io/GOSemSim">GOSemSim</a> for GO semantic similarity measurement</li>
    <li><i class="fa-li fa fa-angle-double-right"></i><a href="https://guangchuangyu.github.io/meshes">meshes</a> for MeSH Enrichment and Semantic analysis</li>
    <li><i class="fa-li fa fa-angle-double-right"></i><a href="https://guangchuangyu.github.io/ReactomePA">ReactomePA</a> for Reactome pathway analysis</li>

</ul>

<p><i class="fa fa-hand-o-right"></i> Find out more on
<a href="https://guangchuangyu.github.io/#projects">projects</a>.</p>
<h2 id="projects-that-depend-on-clusterprofiler"><i class="fa fa-code-fork"></i> Projects that depend on <em>clusterProfiler</em></h2>
<h4 id="bioconductor-packages"><i class="fa fa-angle-double-right"></i> Bioconductor packages</h4>
<ul>
<li><a href="https://www.bioconductor.org/packages/bioCancer">bioCancer</a>:
    Interactive Multi-Omics Cancers Data Visualization and Analysis</li>
<li><a href="https://www.bioconductor.org/packages/debrowser">debrowser</a>:
    Interactive Differential Expresion Analysis Browser</li>
<li><a href="https://www.bioconductor.org/packages/eegc">eegc</a>: Engineering
    Evaluation by Gene Categorization (eegc)</li>
<li><a href="https://www.bioconductor.org/packages/LINC">LINC</a>: co-expression of
    lincRNAs and protein-coding genes</li>
<li><a href="https://www.bioconductor.org/packages/MoonlightR">MoonlightR</a>:
    Identify oncogenes and tumor suppressor genes from omics data</li>
<li><a href="https://www.bioconductor.org/packages/TCGAbiolinks">TCGAbiolinks</a>:
    An R/Bioconductor package for integrative analysis with GDC data</li>
<li><a href="https://www.bioconductor.org/packages/TCGAbiolinksGUI">TCGAbiolinksGUI</a>:
    "TCGAbiolinksGUI: A Graphical User Interface to analyze cancer
    molecular and clinical data"</li>
</ul>
<h4 id="other-applications"><i class="fa fa-angle-double-right"></i> Other applications</h4>
<ul>
<li><a href="https://github.com/bornea/APOSTL">APOSTL</a>: An Interactive Galaxy
    Pipeline for Reproducible Analysis of Affinity Proteomics Data</li>
</ul>
<h2 id="feedback"><i class="fa fa-comment"></i> Feedback</h2>
<ul class="fa-ul">
    <li><i class="fa-li fa fa-hand-o-right"></i> Please make sure you have followed <a href="https://guangchuangyu.github.io/2016/07/how-to-bug-author/"><strong>the important guide</strong></a> before posting any issue/question</li>
    <li><i class="fa-li fa fa-bug"></i> For bugs or feature requests, please post to <i class="fa fa-github-alt"></i> <a href="https://github.com/GuangchuangYu/clusterProfiler/issues">github issue</a></li>
    <li><i class="fa-li fa fa-support"></i>  For user questions, please post to <a href="https://support.bioconductor.org/">Bioconductor support site</a> and <a href="https://www.biostars.org/">Biostars</a>. We are following every post tagged with <strong>clusterProfiler</strong></li>
    <li><i class="fa-li fa fa-commenting"></i> Join the group chat on <a href="https://twitter.com/hashtag/clusterProfiler"><i class="fa fa-twitter fa-lg"></i></a> and <a href="http://huati.weibo.com/k/clusterProfiler"><i class="fa fa-weibo fa-lg"></i></a></li>

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